When comparing Thunar vs Pantheon Files, the Slant community recommends Thunar for most people. In the question“What are the best Linux file managers?”Thunar is ranked 6th while Pantheon Files is ranked 13th. The most important reason people chose Thunar is:

Use Custom Actions to add right-click options to do things like Open as Root, Open Git GUI, etc. You can filter the file types and filename patterns that the actions will show up for.
To add an "Open as Root" action, go to Edit, Configure custom actions. Assign a name and a description. Set Command as "gksudo xdg-open %f" (you'll need to install gksudo since pkexec won't work). Pick an icon (I prefer "changes-allow"). Under Appearance Conditions, select Directories, Text Files, and Other Files.

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Pros

Pro

Custom actions are easy to set up

Use Custom Actions to add right-click options to do things like Open as Root, Open Git GUI, etc. You can filter the file types and filename patterns that the actions will show up for.

To add an "Open as Root" action, go to Edit, Configure custom actions. Assign a name and a description. Set Command as "gksudo xdg-open %f" (you'll need to install gksudo since pkexec won't work). Pick an icon (I prefer "changes-allow"). Under Appearance Conditions, select Directories, Text Files, and Other Files.

Pro

Supports renaming files in bulk

Pro

Can assign custom shortcuts to scripts in XFCE

Thunar can use the editable accelerator feature of XFCE.

Run xfce4-appearance-settings in terminal, go to settings tab, check "enable editable accelerator". Now open any command in Thunar menu, hover to a command, i.e. your custom "places" or your custom command, then press any combination to assign a shortcut to it.be careful tho, cause it will also remove the shortcut from other command.

Pro

Easy to use

Pantheon files (like the Pantheon IDE) is very stylish and minimal. It's minimal and very easy to use. The most useful commands are there in plain sight, on the toolbar or the sidebar.

Cons

Con

Tree sidepane missing features

When the sidepane is in Tree mode, it does not show Places (Favorites). It also doesn't collapse folders (like Windows Explorer), adding to clutter.

Con

Simplified action bar

The action bar on Thunar is very simple and doesn't have as many features and buttons as other file managers. It only has a back, forward, up, and home buttons as well as the folder path.

Con

Requires plugins for some basic functions of modern file managers

Con

Requires GNOME dependencies to support common features

Thunar relies on GVFS to support mounting disks or accessing web folders, however since GVFS is a third party GNOME library and made for the use in the GNOME environment its often incompatible to Thunar stable releases which results into crashes and other issues

Con

No Split View without a patch, which can be a deal breaker

This limitation can be quite annoying indeed.. thanks for the heads up!

Con

Does not integrate well into Gnome

Con

Slightly unstable

Thunar crashes some times on file moves, copy-pasting etc. The developers are working on it, but it's taken a while.

Con

Image thumbnails sometimes wrong

There seems to be a bug where sometimes images get the wrong thumbnail, this can lead to data-loss.

Con

Not very advanced

Pantheon files (like Elementary OS itself) does not offer many advanced features since it's mostly aimed at beginners.